Shaw's plan was to use the Omen Virus to gather
Intersect 3.0

Daniel Shaw with Intersect Glasses

and delete all of the CIA and NSA's intelligence and uploading it into his brain, granting him the Intersect 3.0.

After Daniel Shaw escaped from jail using the Omen Virus and blackmailing Agent Clyde Decker, he captured Sarah and forced Chuck to get the Macau device which would enable him to upload all the data stolen by the Omen Virus into his brain. This would force the government to rehire Shaw and grant him complete power over the government as he would be the only one with access to all their intel.

It is unclear wether the intersect 3.0 grants the user new skills and abilities. (it most likely does because of shaw saying that he has an improved version of the intersect before he fought Chuck.)

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